first commit

help.txt

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+Version: ImageMagick 7.1.0-55 Q16-HDRI aarch64 20670 https://imagemagick.org
+Copyright: (C) 1999 ImageMagick Studio LLC
+License: https://imagemagick.org/script/license.php
+Features: Cipher DPC HDRI Modules OpenMP(5.0) 
+Delegates (built-in): bzlib fontconfig freetype gslib heic jng jp2 jpeg jxl lcms lqr ltdl lzma openexr png ps raw tiff webp xml zlib
+Compiler: gcc (4.2)
+Usage: convert [options ...] file [ [options ...] file ...] [options ...] file
+
+Image Settings:
+  -adjoin              join images into a single multi-image file
+  -affine matrix       affine transform matrix
+  -alpha option        activate, deactivate, reset, or set the alpha channel
+  -antialias           remove pixel-aliasing
+  -authenticate password
+                       decipher image with this password
+  -attenuate value     lessen (or intensify) when adding noise to an image
+  -background color    background color
+  -bias value          add bias when convolving an image
+  -black-point-compensation
+                       use black point compensation
+  -blue-primary point  chromaticity blue primary point
+  -bordercolor color   border color
+  -caption string      assign a caption to an image
+  -clip                clip along the first path from the 8BIM profile
+  -clip-mask filename  associate a clip mask with the image
+  -clip-path id        clip along a named path from the 8BIM profile
+  -colorspace type     alternate image colorspace
+  -comment string      annotate image with comment
+  -compose operator    set image composite operator
+  -compress type       type of pixel compression when writing the image
+  -define format:option
+                       define one or more image format options
+  -delay value         display the next image after pausing
+  -density geometry    horizontal and vertical density of the image
+  -depth value         image depth
+  -direction type      render text right-to-left or left-to-right
+  -display server      get image or font from this X server
+  -dispose method      layer disposal method
+  -dither method       apply error diffusion to image
+  -encoding type       text encoding type
+  -endian type         endianness (MSB or LSB) of the image
+  -family name         render text with this font family
+  -features distance   analyze image features (e.g. contrast, correlation)
+  -fill color          color to use when filling a graphic primitive
+  -filter type         use this filter when resizing an image
+  -font name           render text with this font
+  -format "string"     output formatted image characteristics
+  -fuzz distance       colors within this distance are considered equal
+  -gravity type        horizontal and vertical text placement
+  -green-primary point chromaticity green primary point
+  -illuminant type     reference illuminant
+  -intensity method    method to generate an intensity value from a pixel
+  -intent type         type of rendering intent when managing the image color
+  -interlace type      type of image interlacing scheme
+  -interline-spacing value
+                       set the space between two text lines
+  -interpolate method  pixel color interpolation method
+  -interword-spacing value
+                       set the space between two words
+  -kerning value       set the space between two letters
+  -label string        assign a label to an image
+  -limit type value    pixel cache resource limit
+  -loop iterations     add Netscape loop extension to your GIF animation
+  -matte               store matte channel if the image has one
+  -mattecolor color    frame color
+  -moments             report image moments
+  -monitor             monitor progress
+  -orient type         image orientation
+  -page geometry       size and location of an image canvas (setting)
+  -ping                efficiently determine image attributes
+  -pointsize value     font point size
+  -precision value     maximum number of significant digits to print
+  -preview type        image preview type
+  -quality value       JPEG/MIFF/PNG compression level
+  -quiet               suppress all warning messages
+  -read-mask filename  associate a read mask with the image
+  -red-primary point   chromaticity red primary point
+  -regard-warnings     pay attention to warning messages
+  -remap filename      transform image colors to match this set of colors
+  -repage geometry     size and location of an image canvas
+  -respect-parentheses settings remain in effect until parenthesis boundary
+  -sampling-factor geometry
+                       horizontal and vertical sampling factor
+  -scene value         image scene number
+  -seed value          seed a new sequence of pseudo-random numbers
+  -size geometry       width and height of image
+  -stretch type        render text with this font stretch
+  -stroke color        graphic primitive stroke color
+  -strokewidth value   graphic primitive stroke width
+  -style type          render text with this font style
+  -support factor      resize support: > 1.0 is blurry, < 1.0 is sharp
+  -synchronize         synchronize image to storage device
+  -taint               declare the image as modified
+  -texture filename    name of texture to tile onto the image background
+  -tile-offset geometry
+                       tile offset
+  -treedepth value     color tree depth
+  -transparent-color color
+                       transparent color
+  -undercolor color    annotation bounding box color
+  -units type          the units of image resolution
+  -verbose             print detailed information about the image
+  -view                FlashPix viewing transforms
+  -virtual-pixel method
+                       virtual pixel access method
+  -weight type         render text with this font weight
+  -white-point point   chromaticity white point
+  -write-mask filename associate a write mask with the image  -word-break type     sets whether line breaks appear wherever the text would otherwise overflow
+
+Image Operators:
+  -adaptive-blur geometry
+                       adaptively blur pixels; decrease effect near edges
+  -adaptive-resize geometry
+                       adaptively resize image using 'mesh' interpolation
+  -adaptive-sharpen geometry
+                       adaptively sharpen pixels; increase effect near edges
+  -alpha option        on, activate, off, deactivate, set, opaque, copy
+                       transparent, extract, background, or shape
+  -annotate geometry text
+                       annotate the image with text
+  -auto-gamma          automagically adjust gamma level of image
+  -auto-level          automagically adjust color levels of image
+  -auto-orient         automagically orient (rotate) image
+  -auto-threshold method
+                       automatically perform image thresholding
+  -bench iterations    measure performance
+  -bilateral-blur geometry
+                       non-linear, edge-preserving, and noise-reducing smoothing filter
+  -black-threshold value
+                       force all pixels below the threshold into black
+  -blue-shift factor   simulate a scene at nighttime in the moonlight
+  -blur geometry       reduce image noise and reduce detail levels
+  -border geometry     surround image with a border of color
+  -bordercolor color   border color
+  -brightness-contrast geometry
+                       improve brightness / contrast of the image
+  -canny geometry      detect edges in the image
+  -cdl filename        color correct with a color decision list
+  -channel mask        set the image channel mask
+  -charcoal radius     simulate a charcoal drawing
+  -chop geometry       remove pixels from the image interior
+  -clahe geometry      contrast limited adaptive histogram equalization
+  -clamp               keep pixel values in range (0-QuantumRange)
+  -colorize value      colorize the image with the fill color
+  -color-matrix matrix apply color correction to the image
+  -colors value        preferred number of colors in the image
+  -connected-components connectivity
+                       connected-components uniquely labeled
+  -contrast            enhance or reduce the image contrast
+  -contrast-stretch geometry
+                       improve contrast by 'stretching' the intensity range
+  -convolve coefficients
+                       apply a convolution kernel to the image
+  -cycle amount        cycle the image colormap
+  -decipher filename   convert cipher pixels to plain pixels
+  -deskew threshold    straighten an image
+  -despeckle           reduce the speckles within an image
+  -distort method args
+                       distort images according to given method and args
+  -draw string         annotate the image with a graphic primitive
+  -edge radius         apply a filter to detect edges in the image
+  -encipher filename   convert plain pixels to cipher pixels
+  -emboss radius       emboss an image
+  -enhance             apply a digital filter to enhance a noisy image
+  -equalize            perform histogram equalization to an image
+  -evaluate operator value
+                       evaluate an arithmetic, relational, or logical expression
+  -extent geometry     set the image size
+  -extract geometry    extract area from image
+  -fft                 implements the discrete Fourier transform (DFT)
+  -flip                flip image vertically
+  -floodfill geometry color
+                       floodfill the image with color
+  -flop                flop image horizontally
+  -frame geometry      surround image with an ornamental border
+  -function name parameters
+                       apply function over image values
+  -gamma value         level of gamma correction
+  -gaussian-blur geometry
+                       reduce image noise and reduce detail levels
+  -geometry geometry   preferred size or location of the image
+  -grayscale method    convert image to grayscale
+  -hough-lines geometry
+                       identify lines in the image
+  -identify            identify the format and characteristics of the image
+  -ift                 implements the inverse discrete Fourier transform (DFT)
+  -implode amount      implode image pixels about the center
+  -integral            calculate the sum of values (pixel values) in the image
+  -interpolative-resize geometry
+                       resize image using interpolation
+  -kmeans geometry     K means color reduction
+  -kuwahara geometry   edge preserving noise reduction filter
+  -lat geometry        local adaptive thresholding
+  -level value         adjust the level of image contrast
+  -level-colors color,color
+                       level image with the given colors
+  -linear-stretch geometry
+                       improve contrast by 'stretching with saturation'
+  -liquid-rescale geometry
+                       rescale image with seam-carving
+  -local-contrast geometry
+                       enhance local contrast
+  -mean-shift geometry delineate arbitrarily shaped clusters in the image
+  -median geometry     apply a median filter to the image
+  -mode geometry       make each pixel the 'predominant color' of the
+                       neighborhood
+  -modulate value      vary the brightness, saturation, and hue
+  -monochrome          transform image to black and white
+  -morphology method kernel
+                       apply a morphology method to the image
+  -motion-blur geometry
+                       simulate motion blur
+  -negate              replace every pixel with its complementary color 
+  -noise geometry      add or reduce noise in an image
+  -normalize           transform image to span the full range of colors
+  -opaque color        change this color to the fill color
+  -ordered-dither NxN
+                       add a noise pattern to the image with specific
+                       amplitudes
+  -paint radius        simulate an oil painting
+  -perceptible epsilon
+                       pixel value less than |epsilon| become epsilon or
+                       -epsilon
+  -polaroid angle      simulate a Polaroid picture
+  -posterize levels    reduce the image to a limited number of color levels
+  -profile filename    add, delete, or apply an image profile
+  -quantize colorspace reduce colors in this colorspace
+  -raise value         lighten/darken image edges to create a 3-D effect
+  -random-threshold low,high
+                       random threshold the image
+  -range-threshold values
+                       perform either hard or soft thresholding within some range of values in an image
+  -region geometry     apply options to a portion of the image
+  -render              render vector graphics
+  -resample geometry   change the resolution of an image
+  -resize geometry     resize the image
+  -roll geometry       roll an image vertically or horizontally
+  -rotate degrees      apply Paeth rotation to the image
+  -rotational-blur angle
+                       rotational blur the image
+  -sample geometry     scale image with pixel sampling
+  -scale geometry      scale the image
+  -segment values      segment an image
+  -selective-blur geometry
+                       selectively blur pixels within a contrast threshold
+  -sepia-tone threshold
+                       simulate a sepia-toned photo
+  -set property value  set an image property
+  -shade degrees       shade the image using a distant light source
+  -shadow geometry     simulate an image shadow
+  -sharpen geometry    sharpen the image
+  -shave geometry      shave pixels from the image edges
+  -shear geometry      slide one edge of the image along the X or Y axis
+  -sigmoidal-contrast geometry
+                       increase the contrast without saturating highlights or
+                       shadows
+  -sketch geometry     simulate a pencil sketch
+  -solarize threshold  negate all pixels above the threshold level
+  -sort-pixels         sort each scanline in ascending order of intensity
+  -sparse-color method args
+                       fill in a image based on a few color points
+  -splice geometry     splice the background color into the image
+  -spread radius       displace image pixels by a random amount
+  -statistic type geometry
+                       replace each pixel with corresponding statistic from the
+                       neighborhood
+  -strip               strip image of all profiles and comments
+  -swirl degrees       swirl image pixels about the center
+  -threshold value     threshold the image
+  -thumbnail geometry  create a thumbnail of the image
+  -tile filename       tile image when filling a graphic primitive
+  -tint value          tint the image with the fill color
+  -transform           affine transform image
+  -transparent color   make this color transparent within the image
+  -transpose           flip image vertically and rotate 90 degrees
+  -transverse          flop image horizontally and rotate 270 degrees
+  -trim                trim image edges
+  -type type           image type
+  -unique-colors       discard all but one of any pixel color
+  -unsharp geometry    sharpen the image
+  -vignette geometry   soften the edges of the image in vignette style
+  -wave geometry       alter an image along a sine wave
+  -wavelet-denoise threshold
+                       removes noise from the image using a wavelet transform
+  -white-balance       automagically adjust white balance of image
+  -white-threshold value
+                       force all pixels above the threshold into white
+
+Image Channel Operators:
+  -channel-fx expression
+                       exchange, extract, or transfer one or more image channels
+  -separate            separate an image channel into a grayscale image
+
+Image Sequence Operators:
+  -append              append an image sequence
+  -clut                apply a color lookup table to the image
+  -coalesce            merge a sequence of images
+  -combine             combine a sequence of images
+  -compare             mathematically and visually annotate the difference between an image and its reconstruction
+  -complex operator    perform complex mathematics on an image sequence
+  -composite           composite image
+  -copy geometry offset
+                       copy pixels from one area of an image to another
+  -crop geometry       cut out a rectangular region of the image
+  -deconstruct         break down an image sequence into constituent parts
+  -evaluate-sequence operator
+                       evaluate an arithmetic, relational, or logical expression
+  -flatten             flatten a sequence of images
+  -fx expression       apply mathematical expression to an image channel(s)
+  -hald-clut           apply a Hald color lookup table to the image
+  -layers method       optimize, merge, or compare image layers
+  -morph value         morph an image sequence
+  -mosaic              create a mosaic from an image sequence
+  -poly terms          build a polynomial from the image sequence and the corresponding
+                       terms (coefficients and degree pairs).
+  -print string        interpret string and print to console
+  -process arguments   process the image with a custom image filter
+  -smush geometry      smush an image sequence together
+  -write filename      write images to this file
+
+Image Stack Operators:
+  -clone indexes       clone an image
+  -delete indexes      delete the image from the image sequence
+  -duplicate count,indexes
+                       duplicate an image one or more times
+  -insert index        insert last image into the image sequence
+  -reverse             reverse image sequence
+  -swap indexes        swap two images in the image sequence
+
+Miscellaneous Options:
+  -debug events        display copious debugging information
+  -distribute-cache port
+                       distributed pixel cache spanning one or more servers
+  -help                print program options
+  -list type           print a list of supported option arguments
+  -log format          format of debugging information
+  -version             print version information
+
+By default, the image format of 'file' is determined by its magic
+number.  To specify a particular image format, precede the filename
+with an image format name and a colon (i.e. ps:image) or specify the
+image type as the filename suffix (i.e. image.ps).  Specify 'file' as
+'-' for standard input or output.

presentation.tex

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+\documentclass[t, aspectratio=169, 10pt]{beamer}
+\usepackage{makecell}
+\usepackage{etoolbox}
+\usepackage{biblatex}
+\usepackage{tikz} % for graph
+\usepackage{bbding}
+\usepackage{layouts}
+\usepackage{layout}
+\usepackage{hyperref} % hyper text
+\usepackage{booktabs} % To thicken table lines
+\usepackage[normalem]{ulem} % for striking words
+\usepackage{multicol}
+\usepackage{tikzscale}
+
+% \usepackage[french]{babel} % for date format
+
+
+
+\newcommand{\SubItem}[1]{
+    {\setlength\itemindent{15pt} \item[-] #1}
+}
+
+\newcommand\Wider[2][3em]{%
+\makebox[\linewidth][c]{%
+  \begin{minipage}{\dimexpr\textwidth+#1\relax}
+  \raggedright#2
+  \end{minipage}%
+  }%
+}
+
+%margins
+\newenvironment{changemargin}[2]{%
+\begin{list}{}{%
+\setlength{\topsep}{0pt}%
+\setlength{\leftmargin}{#1}%
+\setlength{\rightmargin}{#2}%
+\setlength{\listparindent}{\parindent}%
+\setlength{\itemindent}{\parindent}%
+\setlength{\parsep}{\parskip}%
+}%
+\item[]}{\end{list}}
+
+% code formating
+\usepackage{xcolor}
+\usepackage{listings} 
+\lstset{basicstyle=\ttfamily,
+  showstringspaces=false,
+  commentstyle=\color{red},
+  keywordstyle=\color{blue}
+}
+
+\definecolor{codegreen}{rgb}{0,0.6,0}
+\definecolor{codegray}{rgb}{0.5,0.5,0.5}
+\definecolor{codepurple}{rgb}{0.58,0,0.82}
+\definecolor{backcolour}{rgb}{0.95,0.95,0.92}
+
+\definecolor{bgturq}{RGB}{35,55,59}
+
+
+\lstdefinestyle{mystyle}{
+  backgroundcolor=\color{backcolour},   
+  commentstyle=\color{codegreen},
+  keywordstyle=\color{magenta},
+  numberstyle=\tiny\color{codegray},
+  stringstyle=\color{codepurple},
+  basicstyle=\ttfamily\footnotesize,
+  breakatwhitespace=false,         
+  breaklines=true,                 
+  captionpos=b,                    
+  keepspaces=true,                 
+  numbers=left,                    
+  numbersep=5pt,                  
+  showspaces=false,                
+  showstringspaces=false,
+  showtabs=false,                  
+  tabsize=2
+}
+
+% ADD '-pdflua' as argument of latexmk
+% Ref https://mirror.ibcp.fr/pub/CTAN/macros/luatex/latex/emoji/emoji-doc.pdf
+\usepackage{emoji}
+% For linux :https://github.com/samuelngs/apple-emoji-linux
+\setemojifont{Apple Color Emoji}
+
+\usepackage[sfdefault]{FiraSans}
+\usetheme{metropolis}           % Use metropolis theme
+\usetikzlibrary{positioning,shapes,arrows,calc,fit,backgrounds,shapes.multipart}
+
+
+\tikzset{box/.style={draw, rectangle, rounded corners, thick, node distance=7em, text width=6em, text centered, minimum height=3.5em}}
+\tikzset{line/.style={draw, thick, -latex'}}
+\tikzset{every node/.style={font=\scriptsize}}
+
+%Graphics and Videos
+% https://tex.stackexchange.com/questions/89088/how-to-embed-video-and-animation-in-latex-and-latex-beamer-step-by-step
+\usepackage{graphicx} %The mode "LaTeX => PDF" allows the following formats: .jpg  .png  .pdf  .mps
+\usepackage{animate}
+
+
+%\usepackage[utf8]{inputenc}
+%\usetheme{Antibes}
+\usefonttheme{professionalfonts}
+
+\setbeamertemplate{itemize items}[circle]
+
+%\bibliography{presentation}
+
+\newcommand\blfootnote[1]{
+  \begingroup
+    \renewcommand\thefootnote{}\footnote{{\tiny #1}}%
+    \addtocounter{footnote}{-1}
+  \endgroup
+}
+
+\newcommand\extrafootertext[1]{%
+    \bgroup
+    \renewcommand\thefootnote{\fnsymbol{footnote}}%
+    \renewcommand\thempfootnote{\fnsymbol{mpfootnote}}%
+    \footnotetext[0]{#1}%
+    \egroup
+}
+%Page de titre:
+\title[]{\emoji{dna} Genetic alterations in ChIP-seq}
+
+\author{Dr. Thomas Steimlé}
+
+\institute[AMU-TAGC]{
+  \vfill
+  \begin{figure}[!b]
+    \vspace{2cm}
+    \centering
+    \includegraphics[height=1.5cm]{Images/amu.png}
+    \hspace*{5cm}
+    \includegraphics[height=1.5cm]{Images/logo_tagc.png}
+  \end{figure}
+}
+\date{\today}
+
+
+%\titlegraphic{\hfill\includegraphics[height=1.5cm]{Images/1200aphp.svg.png}}
+%\logo{\includegraphics[width=3cm]{Images/1200aphp.svg.png}}
+\begin{document}
+
+\begin{frame}
+\maketitle
+\thispagestyle{empty}
+
+\end{frame}
+
+
+\begin{frame}{\emoji{drop-of-blood} Background --- Thymopoiesis}
+  \begin{itemize}
+    \item<1-> During thymopoiesis (HSC $\Rightarrow$ T-cell), the phenotypic diversity of 
+    the antigen receptor (TCR) is acquired.
+  \end{itemize}
+  \centering
+    \includegraphics<1>[width=.4\textwidth]{Images/dev_thym.png}
+    \includegraphics<2>[width=.6\textwidth]{Images/Tcr_str.png}
+\end{frame}
+
+\begin{frame}{\emoji{drop-of-blood} Background --- V(D)J recombination}
+  \begin{itemize}
+    \item<1-> This process involves a series of genome recombination of the different TCR loci 
+    followed by \alert{proliferation selection of functionnal non self-reacting receptors}.
+  \end{itemize}
+  \centering
+    \includegraphics<1>[width=.7\textwidth]{Images/MaturLt.png}
+    \includegraphics<2>[width=.7\textwidth]{Images/TCRBschema.jpg}
+\end{frame}
+
+\begin{frame}{\emoji{dna} Background --- V(D)J recombination}
+  \begin{columns}
+    \begin{column}{.5\textwidth}
+      \begin{itemize}
+        \item V(D)J recombination is a \alert{threat to genomic stability}, 
+        prone to induce \alert{DSB occurring in genes outside of the TCR loci}, 
+        followed by erroneous repair resultating in SV.
+        \item This oncogenesis process is responsible of well known genetic alterations 
+        in T-ALL (particulary translocations accountable of ectopic expression of oncogenes 
+        \textit{TLX1}, \textit{TAL1} etc\dots)$^1$.
+
+        \footnotetext{
+          \tiny
+          1. Larmonie, Nicole S D et al. “Breakpoint sites disclose the role of the V(D)J recombination machinery 
+          in the formation of T-cell receptor (TCR) and non-TCR associated aberrations in T-cell 
+          acute lymphoblastic leukemia.” Haematologica vol. 98,8 (2013): 1173-84
+        }
+      \end{itemize}
+    \end{column}
+    \begin{column}{.6\textwidth}
+      \begin{figure}
+        \centering
+        \includegraphics[width=.8\textwidth]{Images/transloc_oncogenes.png}
+      \end{figure}
+    \end{column}
+  \end{columns}
+\end{frame}
+
+\begin{frame}{\emoji{dna} Background --- T-cell receptor excision circles (TRECs) }
+  \begin{columns}
+    \begin{column}{.5\textwidth}
+      \begin{figure}
+        \includegraphics[width=\textwidth]{Images/trec.png}
+      \end{figure}
+    \end{column}
+    \begin{column}{.5\textwidth}
+      \begin{itemize}
+        \item During recombination deleted parts of the loci are circulized into TRECs.
+        \item Like tansposons the reintegration of TRECs as been suspect to cause 
+        \alert{deregulation of targeted genes}.
+      \end{itemize}
+    \end{column}
+  \end{columns}
+
+  \footnotetext{
+    \tiny
+    Curry, John D et al. “Chromosomal reinsertion of broken RSS ends during T cell development.” The Journal of 
+    experimental medicine vol. 204,10 (2007): 2293-303. doi:10.1084/jem.20070583
+  }
+\end{frame}
+
+{\setbeamercolor{background canvas}{bg=bgturq}
+\begin{frame}[c]
+  \metroset{block=fill}
+  \begin{alertblock}{{\centering \large Hypothesis} }
+    \begin{itemize}
+      \item In T-ALL, we could find with molecular biolgy tools insertions of those TRECs.
+      \item With the same tools we also could also find all the translocations which involves the TCR.
+    \end{itemize}
+  \end{alertblock}
+\end{frame}
+}
+
+\begin{frame}{\emoji{up-arrow} Material \& Method}
+  \begin{itemize}
+    \item<1-> We used our extensed collection of \alert{T-ALL samples at diagnostic n = 1533}.
+    \item<2-> We designed a NGS capture assay with \alert{capture probes} mapped at multiple parts of de TCR \delta { } locus.
+    \item<3-> We developed a specific software to analysed aligned reads and call SV \url{https://github.com/Dr-TSteimle/sv-finder}.
+  \end{itemize}
+  \begin{figure}
+    \centering
+    \includegraphics<2>[width=.8\textwidth]{Images/Probes_TRD.png}
+    \includegraphics<3>[width=.8\textwidth]{Images/assemblage.png}
+  \end{figure}
+\end{frame}
+
+\begin{frame}{\emoji{up-arrow} Results --- \textit{TRD} translocations --- Validation cohort}
+  \begin{itemize}
+    \item To validate our method, we used a previously published cohort of 264 cases analysed with \alert{\textit{TRD} 
+    dual-color FISH probe}$^1$.
+    \item \alert{Se = 98.1\%} [95\% CI 96-99] and \alert{Sp = 97.7\%}
+    \item The 4 FN cases are in fact TRECs insertions inside \textit{ZFP36L2} 
+    that couldn't have been seen with FISH !
+  \end{itemize}
+  \begin{center}
+    \includegraphics[width=.3\textwidth]{Images/confusion.png}
+  \end{center}
+  \vspace{1cm}
+  \footnotetext[1]{
+    \tiny
+    Le Noir, Sandrine et al. “Extensive molecular mapping of TCRα/δ- and TCRβ-involved 
+    chromosomal translocations reveals distinct mechanisms of oncogene activation in T-ALL.” 
+    Blood vol. 120,16 (2012): 3298-309. doi:10.1182/blood-2012-04-425488
+  }
+\end{frame}
+
+\begin{frame}{\emoji{up-arrow} Results --- \textit{TRD} translocations --- Discovery cohort}
+  \begin{figure}
+    \includegraphics[height=.8\textheight]{Images/distribution.png}
+  \end{figure}
+\end{frame}
+
+\begin{frame}{\emoji{dart} Results --- \textit{TRD} translocations --- Discovery cohort}
+  \Wider[4em]{
+    \setlength\columnsep{1pt}
+    \vspace{0.8cm}
+    \begin{multicols}{3}
+      \includegraphics[width=.35\textwidth]{Images/circos_tlx1.png}
+      \includegraphics[width=.35\textwidth]{Images/circos_lmo2.png}
+      \includegraphics[width=.35\textwidth]{Images/circos_tal1.png}
+    \end{multicols}
+  }
+\end{frame}
+
+\begin{frame}{\emoji{dart} Results --- \textit{TRD} translocations --- Discovery cohort}
+  We confirmed all TRECs insertions with sanger sequencing and OGM.
+  \begin{figure}
+    \includegraphics[width=\textwidth]{Images/ZFP36L2_lolli.pdf}
+    \includegraphics[width=\textwidth]{Images/sanger.png}
+    \includegraphics[width=.7\textwidth]{Images/bionano_trec.png}
+  \end{figure}
+\end{frame}
+
+{\setbeamercolor{background canvas}{bg=bgturq}
+\begin{frame}[c]
+  \metroset{block=fill}
+  \vspace{.5cm}
+  \begin{alertblock}{{\centering \large Conclusions} }
+    \begin{itemize}
+      \item We developed a \alert{highly accurate and sensitive method} that enables precise characterization 
+      of \textit{TRD} structural variations. This method can be applied at diagnosis without incurring 
+      any additional costs.
+      \item Our findings provide confirmation that \alert{recurrent TRECs insertions} are present in cases of 
+      T-ALL.
+      \item Using our method, we have observed that these recurrent TRECs insertions predominantly 
+      disrupt the \textit{ZFP36L2} genes.
+      \item The tumor suppressor \textit{ZFP36L2} is well-established to be involved in V(D)J recombination, 
+      but further clarifications are needed regarding its specific role in oncogenesis. Our findings will 
+      help in the characterization of this tumor suppressor.
+    \end{itemize}
+  \end{alertblock}
+\end{frame}
+}
+
+\begin{frame}{\emoji{dart} My PhD --- Rationnal}
+  \begin{itemize}
+    \item The aforementioned results contribute to the understanding of the dysregulation of proto-oncogenes 
+    such as \textit{TAL1}, \textit{TLX1} or \textit{TLX3}.
+    \item Despite extensive investigation, the molecular mechanisms underlying the dysregulation of these oncogenes, 
+    remain elusive in many cases. 
+    \item 
+  \end{itemize}
+\end{frame}
+
+\begin{frame}{\emoji{dart} Troisième année de thèse -- Hypothèses E et F}
+  \begin{itemize}
+   \item Selon les oncogènes identifiés lors des étapes précédentes nous explorerons les possibles interventions thérapeutiques
+   \item Possibilité de test phramacologiques \textit{ex vivo} et \textit{in vivo}. 
+  \end{itemize}
+\end{frame}
+
+% qrencode https://git.t0m4.fr/Thomas/presentation_projet_inserm/raw/master/presentation.pdf -t SVG | sed  's/"#000000"/"#e3b505"/g' | sed 's/"#ffffff"/"#23373B"/g' | /Applications/Inkscape.app/Contents/MacOS/inkscape -p Images/qr-code.pdf
+\begin{frame}[standout]
+  \alert{\textbf{Questions ?}}\\
+  \vspace*{1.5cm}
+  \emoji{calling}
+  \begin{figure}
+    \includegraphics[width=.2\textwidth]{Images/qr-code.pdf}
+  \end{figure}
+\end{frame}
+
+% \begin{frame}
+%   \frametitle{\emoji{floppy-disk} Méthodes > Calling > Lancet}
+%   Source code : \url{https://github.com/nygenome/lancet}
+%   \vskip 0.2in
+%   \lstinputlisting[language=bash, caption={lancet -- bash version}, style=mystyle]{Codes/lancet.txt}
+% \end{frame}
+
+\end{document}